The processing of pre-mRNA to mature mRNA in metazoans is a critical process for the development and normal functioning of cells. The pre-mRNA splicing process involves the removal of intervening sequences from pre-mRNA followed by the ligation of exons to form mature mRNA. This splicing process is catalyzed and regulated by a highly complex macromolecular protein-RNA complex called the spliceosome. The spliceosome is composed of five small nuclear ribonucleoproteins (snRNPs) (U1, U2, U4, U5 and U6) and over 150 associated proteins (Kramer, A. (1996) Anny. Rev. Biochem. 65: 367-409; Wahl et al. (2009) Cell 136: 701-18). The pre-mRNA maturation process includes alternative splicing (AS), which is the mechanism that allows for different forms of mature mRNAs to be generated from the same pre-mRNA. Commonly, alternative splicing patterns determine the inclusion or exclusion of portions of the coding sequence in the mRNA, giving rise to protein isoforms that differ in their peptide sequence. Alternate splicing is regulated by numerous spliceosomal trans-acting proteins, which are in turn regulated by cis-acting regulatory sites on pre-mRNA substrates (Kramer, A. (1996) Anny. Rev. Biochem. 65: 367-409). Since pre-mRNAs for a given gene may contain many different exon and intron combinations, there are often a very large number of possible mRNAs that can lead to a correspondingly large set of proteins with different, even opposing, biological functions within the cell. The complexity of the spliceosome and the current scarcity of molecular-resolution X-ray structures complicates a rapid advancement in the understanding of many of the important functional mechanisms that are critical to the normal functioning of the cells of higher organisms (Yan et al. (2015) Science 349: 1182-1191). Because of the importance of splicing in normal organismal development, the spliceosome is increasingly being recognized as a major frontier for molecular biology and is now accepted as a valid oncology target (Webb et al. (2013) Drug Discovery Today 18: 43-49; Bonnal et al. (2012) Nat. Rev. Drug Discov. 11: 847-859).
Interest in the spliceosome was dramatically bolstered when two independent groups reported that a pair of structurally divergent bacterial natural products, FR901464 and pladienolide, both target a similar site on the SF3B subunit of the spliceosome (Kaida et al. (2007) Nat. Chem. Biol. 3: 576-83; Kotake et al. (2007) Nat. Chem. Biol. 3: 570-5). Subsequent to those initial discoveries, the list of compounds that are known to target the SF3B subunit has grown to include additional bacterial natural products such as herboxidiene (GEX1A) (isolated from Streptomyces sp. A7847) (Hasegawa et al. (2011) ACS Chem. Biol. 6: 229-33) and the thailanstatins (isolated from Burkholderia thailandensis) (Liu et al. (2013) Journal of Natural Products 76: 685-693). These bacterial fermentation products show cytotoxic IC50s in the low nanomolar range in tumor cell lines and were reported to have a similar distinctive effect on the cell cycle in mammalian cell lines, which includes cell cycle arrest in the G1 and G2/M phases (Nakajima et al. (1996) J. Antibiot. (Tokyo) 49: 1196-203). Several of these natural products have also been reported to show potent antitumor activity in vitro and in vivo (Nakajima et al. (1996) J. Antibiot. (Tokyo) 49: 1204-11; Mizui et al. (2004) J. Antiobiot. (Tokyo) 57: 188-96). Work in this area led to the development of the semisynthetic pladienolide analog E7107 that entered Phase I clinical studies (Kotake et al. (2007) Nat. Chem. Biol. 3: 570-5; Eskens et al. (2013) Clin. Cancer Res. 19: 6296-304; Yoshida et al. (2011) Nature 478: 64-9), without the benefit of many subsequent recent discoveries relevant to mechanism of action, tumor selectivity, and patient stratification (Webb et al. (2013) Drug Discovery Today 18: 43-49; Bonnal et al. (2012) Nat. Rev. Drug Discov. 11: 847-859).
Despite the increased interest in the spliceosome as a target for cancer therapeutics, small molecules that target specific sites on the spliceosome have thus far remained elusive. Therefore, there remains a need for the identification of new oncology drug targets and new small-molecule therapeutic leads for the diagnosis and treatment of multiple forms of cancer and other diseases involving aberrant spliceosome activities. These needs and others are met by the present invention.